manulera / pombase_gtf_file

A script to convert pombase gff3 file into GFT format compatible with transvar.
MIT License
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PomBase GTF file

A script to convert pombase gff3 file into GFT format compatible with transvar.

Requirements for running using docker

You need to have docker installed. Then simply run: bash run_with_docker.sh

The output gtf file will be at data/pombase_genome.gtf.

What it does:

Requirements for running locally

Install python dependencies and activate virtual env:

poetry install
poetry shell

See the file run_locally.sh, which downloads and installs several dependencies if not present:

You can install them with brew or apt otherwise

# If you have linux and you want to install them globally
sudo apt install -y samtools tabix gffread

# Installing globally in mac
brew install htslib samtools gffread

Then runs bioconvert as well as the python script.